PMC

Maximum-likelihood phylogenetic tree for genus Prunus L. based on 14 complete chloroplast genomes. The number on each node indicates bootstrap support value >50% for each clade. Accession Numbers: Prunus kansuensis (KF990036), Prunus davidiana (MK634746), P. persica (HQ336405), Prunus mongolica (MG602256), Prunus armeniaca (KY420025), Prunus pedunculata (MG602257), Prunus salicina (KY420002), Prunus yedoensis (KU985054), Prunus conradinae (KY419991), Prunus pseudocerasus (KX255667), Prunus undulata (KY420035), Prinsepia utilis (KC571835), Prinsepia sinensis (KY419985).

Phylogenetic tree inferred by maximum-likelihood (ML) method based on the complete chloroplast genomes of 30 Prunus species and one outlier (Malus baccata). For clearly displaying the phylogenetic relationship, a cladogram without species name is placed in the top left. A total of 1000 bootstrap replicates were performed, and the bootstrap support values (percentage) are indicated behind nodes. The chloroplast genome of Prunus salicina cultivar Zuili is shown in bold. The NCBI GenBank accession numbers are shown in parentheses. The gray lines were used to supplement the branch length, and the branch length of the phylogram was black. The following sequences were used: Prunus salicina ‘Wanshuangcuili’ MW406460.1, Prunus salicina ‘Jincuili’ MW406467.1, Prunus salicina ‘Yinhongli’ MW406465.1, Prunus salicina ‘Cuihongli’ MW406468.1, Prunus salicina ‘Sanhuali’ MW406459.1, Prunus salicina ‘Wuyuecui’ MW406461.1, Prunus salicina ‘No.2 Guofeng’ MW406472.1, Prunus salicina ‘Qingnai MW406469.1, Prunus salicina OM256485.1 (Su et al. ), Prunus domestica NC_050959.1 (Geng et al. ), Prunus mandshurica NC_068703.1, Prunus zhengheensis NC_062793.1, Prunus tenella NC_044965.1, Prunus dictyoneura NC_051894.1 (Liu et al. ), Prunus japonica NC_053703.1 (Mu et al. ), Prunus persica NC_014697.1 (Jansen et al. ), Prunus ussuriensis NC_065730.1, Prunus kansuensis NC_023956.1, Prunus mira NC_040125.1 (Bao et al. ), Prunus davidiana NC_039735.1 (Zhang et al. ), Prunus stipulacea NC_068705.1, Prunus discadenia NC_056362.1, Prunus polytricha NC_072948.1, Prunus serrula NC_072949.1, Prunus conadenia NC_072946.1, Prunus verecunda NC_053694.1 (Jiang et al. ), Prunus yunnanensis NC_072950.1, Prunus mugus NC_072947.1, Prunus zippeliana NC_043926.1, and Malus baccata NC_045389.1.

Distribution of putative encoded amino acids in Prunus species: Prunus persica (a), Prunus armeniaca (b), Prunus avium (c), Prunus mume (d), Prunus dulcis (e), and Prunus cerasus (f)

The estimation of divergence time and expansion or contraction of gene families in Prunus mume, Prunus apricot, Prunus salicina, Prunus persica v2.0, CN14 (Prunus persica L.), Prunus dulcis, Prunus communis, Malus × domestica, Rose chinensis, Carica papaya, Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa.